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Journal of Bioinformatics and Computational Biology

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https://www.readbyqxmd.com/read/28317416/editorial-bioinformatics-development-at-the-bgrs-sb-conference-series-10th-anniversary
#1
Yuriy L Orlov, Nikolay A Kolchanov, Ralf Hofest├Ądt, Limsoon Wong
No abstract text is available yet for this article.
March 20, 2017: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/28345370/an-accurate-and-fast-alignment-free-method-for-profiling-microbial-communities
#2
Diem-Trang Pham, Shanshan Gao, Vinhthuy Phan
Determining abundances of microbial genomes in metagenomic samples is an important problem in analyzing metagenomic data. Although homology-based methods are popular, they have shown to be computationally expensive due to the alignment of tens of millions of reads from metagenomic samples to reference genomes of hundreds to thousands of environmental microbial species. We introduce an efficient alignment-free approach to estimate abundances of microbial genomes in metagenomic samples. The approach is based on solving linear and quadratic programs, which are represented by genome-specific markers (GSM)...
March 7, 2017: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/28335678/computational-study-on-transfer-of-l-ascorbic-acid-by-ulaa-through-escherichia-coli-membrane
#3
Ehsan Faghih-Mirzaee, Maryam Dehestani, Leila Zeidabadinejad
In this study, the transfer of L-ascorbic acid by UlaA through Escherichia coli (E. coli) membrane was evaluated using density functional theory (DFT), molecular docking, and molecular dynamics (MD) simulation methods. DFT calculations at the B3lyp/6[Formula: see text]311[Formula: see text]G(p,d) level were performed to investigate the interaction properties and molecular descriptors. The physical properties, such as chemical potential, chemical hardness, and chemical electrophilicity of all studied molecules, were investigated...
February 24, 2017: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/28274175/the-origins-and-evolutionary-history-of-human-non-coding-rna-regulatory-networks
#4
Masih Sherafatian, Seyed Javad Mowla
The evolutionary history and origin of the regulatory function of animal non-coding RNAs are not well understood. Lack of conservation of long non-coding RNAs and small sizes of microRNAs has been major obstacles in their phylogenetic analysis. In this study, we tried to shed more light on the evolution of ncRNA regulatory networks by changing our phylogenetic strategy to focus on the evolutionary pattern of their protein coding targets. We used available target databases of miRNAs and lncRNAs to find their protein coding targets in human...
February 1, 2017: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/28274174/samira-vp-a-simple-protein-alignment-method-with-rechecking-the-alphabet-vector-positions
#5
Samira Fotoohifiroozabadi, Mohd Saberi Mohamad, Safaai Deris
Protein structure alignment and comparisons that are based on an alphabetical demonstration of protein structure are more simple to run with faster evaluation processes; thus, their accuracy is not as reliable as three-dimension (3D)-based tools. As a 1D method candidate, TS-AMIR used the alphabetic demonstration of secondary-structure elements (SSE) of proteins and compared the assigned letters to each SSE using the [Formula: see text]-gram method. Although the results were comparable to those obtained via geometrical methods, the SSE length and accuracy of adjacency between SSEs were not considered in the comparison process...
January 26, 2017: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/28110602/sitex-2-0-projections-of-protein-functional-sites-on-eukaryotic-genes-extension-with-orthologous-genes
#6
Irina V Medvedeva, Pavel S Demenkov, Vladimir A Ivanisenko
Functional sites define the diversity of protein functions and are the central object of research of the structural and functional organization of proteins. The mechanisms underlying protein functional sites emergence and their variability during evolution are distinguished by duplication, shuffling, insertion and deletion of the exons in genes. The study of the correlation between a site structure and exon structure serves as the basis for the in-depth understanding of sites organization. In this regard, the development of programming resources that allow the realization of the mutual projection of exon structure of genes and primary and tertiary structures of encoded proteins is still the actual problem...
January 23, 2017: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/28238281/new-multilocus-linkage-disequilibrium-measure-for-tag-snp-selection
#7
Bo Liao, Xiangjun Wang, Wen Zhu, Xiong Li, Lijun Cai, Haowen Chen
Numerous approaches have been proposed for selecting an optimal tag single-nucleotide polymorphism (SNP) set. Most of these approaches are based on linkage disequilibrium (LD). Classical LD measures, such as D' and r(2), are frequently used to quantify the relationship between two marker (pairwise) linkage disequilibria. Despite of their successful use in many applications, these measures cannot be used to measure the LD between multiple-marker. These LD measures need information about the frequencies of alleles collected from haplotype dataset...
February 2017: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/28201946/sorting-permutations-by-prefix-and-suffix-rearrangements
#8
Carla Negri Lintzmayer, Guillaume Fertin, Zanoni Dias
Some interesting combinatorial problems have been motivated by genome rearrangements, which are mutations that affect large portions of a genome. When we represent genomes as permutations, the goal is to transform a given permutation into the identity permutation with the minimum number of rearrangements. When they affect segments from the beginning (respectively end) of the permutation, they are called prefix (respectively suffix) rearrangements. This paper presents results for rearrangement problems that involve prefix and suffix versions of reversals and transpositions considering unsigned and signed permutations...
February 2017: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/28178889/v-elmpirnapred-identification-of-human-pirnas-by-the-voting-based-extreme-learning-machine-v-elm-with-a-new-hybrid-feature
#9
Cong Pian, Yuan-Yuan Chen, Jin Zhang, Zhi Chen, Guang-Le Zhang, Qiang Li, Tao Yang, Liang-Yun Zhang
Piwi-interacting RNAs (piRNAs) were recently discovered as endogenous small noncoding RNAs. Some recent research suggests that piRNAs may play an important role in cancer. So the precise identification of human piRNAs is a significant work. In this paper, we introduce a series of new features with 80 dimension called short sequence motifs (SSM). A hybrid feature vector with 1444 dimension can be formed by combining 1364 features of [Formula: see text]-mer strings and 80 features of SSM features. We optimize the 1444 dimension features using the feature score criterion (FSC) and list them in descending order according to the scores...
February 2017: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/28178888/histone-modifications-influence-skipped-exons-inclusion
#10
Yue Hou, Huan Huang, Wenqiao Hu, Hongde Liu, Xiao Sun
Alternative splicing (AS), by which individual genes can produce multiple mRNA, associates with genomic complexity, disease, and development. Histone modifications show important roles in both transcription initiation and mRNA splicing. Here, we intended to find the link between AS and histone modifications in flanking regions through analyzing publicly available data in two human cell lines, GM12878 and K562 cell lines. According to exon inclusion levels, exons were classified into three types, included skipped exons, excluded skipped exons and expressed constitutive exons...
February 2017: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/28150521/drug-repurposing-and-therapeutic-anti-microrna-predictions-for-inhibition-of-oxidized-low-density-lipoprotein-induced-vascular-smooth-muscle-cell-associated-diseases
#11
Shun-Tsung Chen, Chien-Hung Huang, Victor C Kok, Chi-Ying F Huang, Jin-Shuei Ciou, Jeffrey J P Tsai, Nilubon Kurubanjerdjit, Ka-Lok Ng
Drug repurposing is a new method for disease treatments, which accelerates the identification of new uses for existing drugs with minimal side effects for patients. MicroRNA-based therapeutics are a class of drugs that have been used in gene therapy following the FDA's approval of the first anti-sense therapy. This study examines the effects of oxLDL on vascular smooth muscle cells (VSMCs) and identifies potential drugs and antimiRs for treating VSMC-associated diseases. The Connectivity Map (cMap) database is utilized to identify potential new uses of existing drugs...
February 2017: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/27989220/mathematical-model-of-lsrr-binding-and-derepression-in-escherichia-coli-k12
#12
Steven M Graff, William E Bentley
Quorum sensing (QS) enables bacterial communication and collective behavior in response to self-secreted signaling molecules. Unlocking its genetic regulation will provide insight towards understanding its influence on pathogenesis, formation of biofilms, and many other phenotypes. There are few datasets available that link QS-mediated gene expression to its regulatory components and even fewer mathematical models that incorporate known mechanistic detail. By integrating these data with annotated sequence information, mathematical inferences can be pieced together that shed light on regulatory structure...
February 2017: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/27899048/the-method-for-breast-cancer-grade-prediction-and-pathway-analysis-based-on-improved-multiple-kernel-learning
#13
Tianci Song, Yan Wang, Wei Du, Sha Cao, Yuan Tian, Yanchun Liang
Breast cancer histologic grade represents the morphological assessment of the tumor's malignancy and aggressiveness, which is vital in clinically planning treatment and estimating prognosis for patients. Therefore, the prediction of breast cancer grade can markedly elevate the detection of early breast cancer and efficiently guide its treatment. With the advent of high-throughput profiling technology, a large number of data of different types are rapidly generated, and each data provides its unique biological insight...
February 2017: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/27411307/a-machine-learning-approach-for-predicting-palmitoylation-sites-from-integrated-sequence-based-features
#14
Liqi Li, Qifa Luo, Weidong Xiao, Jinhui Li, Shiwen Zhou, Yongsheng Li, Xiaoqi Zheng, Hua Yang
Palmitoylation is the covalent attachment of lipids to amino acid residues in proteins. As an important form of protein posttranslational modification, it increases the hydrophobicity of proteins, which contributes to the protein transportation, organelle localization, and functions, therefore plays an important role in a variety of cell biological processes. Identification of palmitoylation sites is necessary for understanding protein-protein interaction, protein stability, and activity. Since conventional experimental techniques to determine palmitoylation sites in proteins are both labor intensive and costly, a fast and accurate computational approach to predict palmitoylation sites from protein sequences is in urgent need...
February 2017: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/27397631/an-improved-method-for-predicting-interactions-between-virus-and-human-proteins
#15
Byungmin Kim, Saud Alguwaizani, Xiang Zhou, De-Shuang Huang, Byunkyu Park, Kyungsook Han
The interaction of virus proteins with host proteins plays a key role in viral infection and consequent pathogenesis. Many computational methods have been proposed to predict protein-protein interactions (PPIs), but most of the computational methods are intended for PPIs within a species rather than PPIs across different species such as virus-host PPIs. We developed a method that represents key features of virus and human proteins of variable length into a feature vector of fixed length. The key features include the relative frequency of amino acid triplets (RFAT), the frequency difference of amino acid triplets (FDAT) between virus and host proteins, and amino acid composition (AC)...
February 2017: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/28033736/introductory-note-for-jbcb-special-issue
#16
Chandra Verma, Peter Bond
No abstract text is available yet for this article.
December 30, 2016: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/28152643/a-study-of-structural-properties-of-gene-network-graphs-for-mathematical-modeling-of-integrated-mosaic-gene-networks
#17
Olga V Petrovskaya, Evgeny D Petrovskiy, Inna N Lavrik, Vladimir A Ivanisenko
Gene network modeling is one of the widely used approaches in systems biology. It allows for the study of complex genetic systems function, including so-called mosaic gene networks, which consist of functionally interacting subnetworks. We conducted a study of a mosaic gene networks modeling method based on integration of models of gene subnetworks by linear control functionals. An automatic modeling of 10,000 synthetic mosaic gene regulatory networks was carried out using computer experiments on gene knockdowns/knockouts...
December 22, 2016: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/28073302/is-the-average-shortest-path-length-of-gene-set-a-reflection-of-their-biological-relatedness
#18
Varsha Embar, Adam Handen, Madhavi K Ganapathiraju
When a set of genes are identified to be related to a disease, say through gene expression analysis, it is common to examine the average distance among their protein products in the human interactome as a measure of biological relatedness of these genes. The reasoning for this is that, genes associated with a disease would tend to be functionally related, and that functionally related genes would be closely connected to each other in the interactome. Typically, average shortest path length (ASPL) of disease genes (although referred to as genes in the context of disease-associations, the interactions are among protein-products of these genes) is compared to ASPL of randomly selected genes or to ASPL in a randomly permuted network...
December 2016: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/28073301/author-index-volume-14-2016
#19
(no author information available yet)
No abstract text is available yet for this article.
December 2016: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/27774871/phrased-ml-a-paraphrased-human-readable-adaptation-of-sed-ml
#20
Kiri Choi, Lucian P Smith, J Kyle Medley, Herbert M Sauro
MOTIVATION: Model simulation exchange has been standardized with the Simulation Experiment Description Markup Language (SED-ML), but specialized software is needed to generate simulations in this format. Text-based languages allow researchers to create and modify experimental protocols quickly and easily, and export them to a common machine-readable format. RESULTS: phraSED-ML language allows modelers to use simple text commands to encode various elements of SED-ML (models, tasks, simulations, and results) in a format easy to read and modify...
December 2016: Journal of Bioinformatics and Computational Biology
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